For each of the 45 analyzed traits, we release one file containing summary statistics computed by BOLT-LMM for all genetic variants analyzed for that trait.

Each file name is structured as ${trait_name}"hg38_liftover_sumstats.bgen.stats.gz".

Each file is a standard BOLT-LMM output file (https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html). Each file contains a line for each genetic variant. For each genetic variant, we report its name, chromosome,  position in hg38 (lifted over from hg19), allele 1, allele 0, INFO score, chi-squared statistic from linear regression, pvalue from linear regression, beta from BOLT-LMM INF, standard error (SE) from BOLT-LMM INF, chi-squared statistic from BOLT-LMM INF, p-value from BOLT-LMM INF, Chi-squared statistic from BOLT-LMM, and p-value from BOLT-LMM. 

Z-scores for the TGFM analysis were computed from the Bolt-LMM output as follows. As the noninfinitesimal version of BOLT-LMM does not calculate effect sizes, we calculated z-scores by taking the square root of the BOLT-LMM chi-squared statistics and multiplying them by the sign of the effect size estimate from the infinitesimal version of BOLT-LMM.